7B4N: Cellular tumor antigen p53

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human wild-type p53DBD bound to DNA and MQ: wt-DNA-MQ (II). Determined by X-ray diffraction at 1.32 Å resolution. Released 8 Dec 2021.

Method: X-ray diffraction
Resolution: 1.32 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,300
Mol. weight: 26.75 kDa
Ligands: ZN, QN8, QNN
Released: 8 Dec 2021

Explore 7B4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B4N contains 7 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	98-99	2
β-strand	103	1	1
β-strand	110-112	3	2
β-strand	124-127	4	1
β-strand	132-135	4	1
β-strand	140-146	7	2
α-helix	150-152	3
β-strand	156-163	8	1
α-helix	166-168	3
α-helix	172-173	2
α-helix	177-181	5
β-strand	195-198	4	2
β-strand	204-207	4	1
β-strand	214-219	6	1
α-helix	222-224	3
β-strand	230-236	7	2
β-strand	251-258	8	1
β-strand	264-274	11	1
α-helix	278-292	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cellular tumor antigen p53	A	protein	200	Homo sapiens	P04637 (AlphaFold model)
DNA target	B	DNA	12	synthetic construct

Sequence of entity 1 (A), FASTA

>7B4N_1 Cellular tumor antigen p53 (chains A)
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPP
GTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVR
VCACPGRDRRTEEENLRKKG

Sequence of entity 2 (B), FASTA

>7B4N_2 DNA target (chains B)
CGGGCATGCCCG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
QN8	(2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one	C8 H13 N O	2
QNN	(2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one	C8 H13 N O	1

Water and common crystallization additives (FMT) are not listed.

Primary citation

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Degtjarik, O., Golovenko, D., Diskin-Posner, Y. et al. Nat Commun (2021) 12:7057-7057. DOI 10.1038/s41467-021-27142-6 · PubMed

Other PDB entries of the same protein (UniProt P04637 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9C5S 1.01 Å, Disulfide-linked, antiparallel p53-derived peptide dimer (CV1)
3D06 1.2 Å, Human p53 core domain with hot spot mutation R249S (I)
5MHC 1.2 Å, Crystal structure of 14-3-3sigma and a p53 C-terminal 12-mer synthetic phosphopeptide
8UQR 1.22 Å, Crystal structure of the human p53 tetramerization domain
6GGC 1.24 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9320
6SHZ 1.24 Å, p53 cancer mutant Y220C
4MZI 1.25 Å, Crystal structure of a human mutant p53
6GGE 1.25 Å, p53 cancer mutant Y220C in complex with small-molecule stabilizer PK9327
3LW1 1.28 Å, Binary complex of 14-3-3 sigma and p53 pT387-peptide
5O1E 1.3 Å, p53 cancer mutant Y220C im complex with compound MB577
6RL3 1.3 Å, Fragment AZ-003 binding at the p53pT387/14-3-3 sigma interface
8E7A 1.3 Å, Crystal structure of the p53 (Y107H) core domain orthorhombic P form

Browse structure collections

About this viewer

MolViewer shows 7B4N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.